Variant report

Variant	rs11125169
Chromosome Location	chr2:48591889-48591890
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11125170	0.90[CEU][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17037291	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs17325488	0.84[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57729372	0.84[EUR][1000 genomes]
rs60527991	0.95[EUR][1000 genomes]
rs61062762	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62137000	0.83[EUR][1000 genomes]
rs62137013	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7563625	0.90[CEU][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv874001	chr2:48534363-48624007	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv874002	chr2:48547751-48610367	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
4	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv874003	chr2:48570509-48619869	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11125169	CCDC128	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48571200-48605200	Weak transcription	Colonic Mucosa	Colon
2	chr2:48572200-48597000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:48573600-48604000	Weak transcription	Ovary	ovary
4	chr2:48574200-48602000	Weak transcription	Gastric	stomach
5	chr2:48574600-48602000	Weak transcription	Small Intestine	intestine
6	chr2:48576200-48597000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:48576200-48602000	Weak transcription	Lung	lung
8	chr2:48576600-48595600	Weak transcription	Fetal Brain Female	brain
9	chr2:48576600-48602000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:48577800-48592400	Weak transcription	Right Atrium	heart
11	chr2:48577800-48602000	Weak transcription	Fetal Kidney	kidney
12	chr2:48577800-48603800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:48578600-48604800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:48579000-48595000	Weak transcription	Esophagus	oesophagus
15	chr2:48579000-48595000	Weak transcription	Fetal Stomach	stomach
16	chr2:48579200-48593000	Weak transcription	Fetal Muscle Leg	muscle
17	chr2:48579200-48595400	Weak transcription	Fetal Intestine Large	intestine
18	chr2:48580400-48595200	Weak transcription	HSMMtube	muscle
19	chr2:48580600-48601800	Weak transcription	Hela-S3	cervix
20	chr2:48580800-48599800	Weak transcription	NHEK	skin
21	chr2:48580800-48602000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr2:48580800-48602000	Weak transcription	Osteobl	bone
23	chr2:48580800-48604000	Weak transcription	Aorta	Aorta
24	chr2:48581000-48593400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:48581400-48592400	Weak transcription	NHDF-Ad	bronchial
26	chr2:48581400-48600800	Weak transcription	Spleen	Spleen
27	chr2:48581400-48601800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr2:48581400-48602000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr2:48581400-48602000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr2:48581400-48608000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr2:48581800-48602000	Weak transcription	Pancreas	Pancrea
32	chr2:48581800-48602000	Weak transcription	Right Ventricle	heart
33	chr2:48581800-48604800	Weak transcription	Psoas Muscle	Psoas
34	chr2:48582000-48600800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr2:48584400-48602000	Weak transcription	Brain Angular Gyrus	brain
36	chr2:48584600-48601000	Weak transcription	Fetal Lung	lung
37	chr2:48584800-48593600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:48584800-48604400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:48585000-48600600	Weak transcription	HUVEC	blood vessel
40	chr2:48585600-48598000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr2:48586000-48595800	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr2:48586000-48596000	Strong transcription	Primary B cells from peripheral blood	blood
43	chr2:48586000-48602000	Weak transcription	Brain Germinal Matrix	brain
44	chr2:48587000-48598400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:48587600-48596400	Strong transcription	HSMM	muscle
46	chr2:48587800-48593200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr2:48588000-48602000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:48588200-48593200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr2:48588200-48597800	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr2:48588400-48596600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links